- Undergraduate Education
- B.S., B.M. University of Wyoming (1995)
- Graduate Education
- Postdoc. University of California, San Francisco (2003-2008)
- Joined Texas A&M in 2008
- NSF CAREER Award 2013
Evolution of Protein Structure and Function
Evolution is the organizing principle of biology and provides the cornerstone of our approach to understand the relationships between protein structure and function. We combine bioinformatics, biochemistry, and genetics to address fundamental questions about protein evolution, such as: What structural and mechanistic features of enzymes increase their capacity to evolve new functions? How do new metabolic pathways evolve? Are there multiple evolutionary pathways to evolve new enzyme activities?
Our primary focus is on how catalytic promiscuity serves as the raw material for evolving new enzyme activities. Catalytic promiscuity is the ability to catalyze different chemical reactions using the same active site. Many enzymes in one branch of the protein family we are studying are catalytically promiscuous, and this activity has been incorporated into new metabolic pathways more than once. Comparing the sequences and structures of these proteins will identify characteristics that permitted them to evolve the second activity.
Our goal is to use results from our research to identify fundamental evolutionary principles that can can help decipher protein structure-function relationships, predict protein functions, and improve protein engineering methods.
Odokonyero, D, McMillan, AW, Ramagopal, UA, Toro, R, Truong, DP, Zhu, M et al.. Comparison of Alicyclobacillus acidocaldarius o-Succinylbenzoate Synthase to Its Promiscuous N-Succinylamino Acid Racemase/ o-Succinylbenzoate Synthase Relatives. Biochemistry. 2018;57 (26):3676-3689.
Glasner, ME. Finding enzymes in the gut metagenome. Science. 2017;355 (6325):577-578.
McMillan, AW, Lopez, MS, Zhu, M, Morse, BC, Yeo, IC, Amos, J et al.. Role of an active site loop in the promiscuous activities of Amycolatopsis sp. T-1-60 NSAR/OSBS. Biochemistry. 2014;53 (27):4434-44.
Brizendine, AM, Odokonyero, D, McMillan, AW, Zhu, M, Hull, K, Romo, D et al.. Promiscuity of Exiguobacterium sp. AT1b o-succinylbenzoate synthase illustrates evolutionary transitions in the OSBS family. Biochem. Biophys. Res. Commun. 2014;450 (1):679-84.
Odokonyero, D, Sakai, A, Patskovsky, Y, Malashkevich, VN, Fedorov, AA, Bonanno, JB et al.. Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family. Proc. Natl. Acad. Sci. U.S.A. 2014;111 (23):8535-40.
Odokonyero, D, Ragumani, S, Lopez, MS, Bonanno, JB, Ozerova, ND, Woodard, DR et al.. Divergent evolution of ligand binding in the o-succinylbenzoate synthase family. Biochemistry. 2013;52 (42):7512-21.
Zhu, WW, Wang, C, Jipp, J, Ferguson, L, Lucas, SN, Hicks, MA et al.. Residues required for activity in Escherichia coli o-succinylbenzoate synthase (OSBS) are not conserved in all OSBS enzymes. Biochemistry. 2012;51 (31):6171-81.
Sakai, A, Fedorov, AA, Fedorov, EV, Schnoes, AM, Glasner, ME, Brown, S et al.. Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes. Biochemistry. 2009;48 (7):1445-53.
Pieper, U, Chiang, R, Seffernick, JJ, Brown, SD, Glasner, ME, Kelly, L et al.. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. J. Struct. Funct. Genomics. 2009;10 (2):107-25.
Kalyanaraman, C, Imker, HJ, Fedorov, AA, Fedorov, EV, Glasner, ME, Babbitt, PC et al.. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure. 2008;16 (11):1668-77.